[Bioperl-l] Bio::Ontology::OntologyI

[Naama Menda]

On Sun, Mar 9, 2008 at 10:43 PM, Hilmar Lapp <hlapp at gmx.net> wrote:

>
> On Mar 9, 2008, at 10:26 PM, Naama Menda wrote:
>
>
> On Sun, Mar 9, 2008 at 10:13 PM, Hilmar Lapp <hlapp at gmx.net> wrote:
>
> >
> > On Mar 9, 2008, at 9:34 PM, Naama Menda wrote:
> >
> > My main problem is that go-perl does not handle updates, so if I want to
> > update GO I need an empty schema. We find it more complicated to re-load our
> > annotations than to update cvterms and their related data.
> > Our loading script compares an existing load of an ontology to the obo
> > file and updates/insets/deletes accordingly.
> >
> >
> > load_ontology.pl in bioperl-db should have all this functionality,
> > though of course that doesn't give you the typedef support (yet).
> >
>
> Will you add this support to obo.pm? I had a look at it and it seems easy
> to implement.
> Will there be a patch? Or in the next Bioperl release?
>
>
> If you have ideas for how to implement this we'd be thrilled if you can
> provide a patch.
>
> Most changes in BioPerl happen because and by people who have an itch to
> scratch. Seems like this one is right down your alley?
>
> I'd in principle be interested in doing this too but can't give any
> promises as to when I might have time (unless I need it myself :)
>

I'll try to provide a patch for this. I'll let you know how it goes..

>
>
>
> >
> > We are now in the process of committing this code to GMOD
> >
> >
> > Cool - obviously load_ontology.pl doesn't work off of Chado but instead
> > uses BioSQL as the schema (though the ontology model is *very* similar
> > between the two).
> >
>
> We  store ontologies in Chado, and that was the reason for writing a new
> loader.
>
>
> Looking at it it seems you wrote a whole new language binding? Did you
> find it too difficult to build on one of the existing ones (which use
> Class::DBI if I recall correctly, though Scott will have the details here)
>

We already had most of the classes. We use these for other code at SGN,
since it's all OO perl. All we needed to do is to add some methods and
accessors to  our Chado classes, and  write a loading script that stores the
ontology from the db and the ontology from the file in hashrefs, compare the
2 and insert/update accordingly. Our main concern was for updating
pre-loaded ontologies (for new ontology files GMOD's make-ontologies works
great!)


> -hilmar
>
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
> -Naama